2WMZ

Structure of a mutated TolC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Sequential Open States in a Symmetrical Opening Transition of the Tolc Exit Duct.

Pei, X.Y.Hinchliffe, P.Symmons, M.F.Koronakis, E.Benz, R.Hughes, C.Koronakis, V.

(2011) Proc.Natl.Acad.Sci.USA 108: 2112

  • DOI: 10.1073/pnas.1012588108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In bacterial drug resistance and virulence pumps, an inner membrane (IM) transporter and periplasmic adaptor recruit an outer membrane (OM) trimeric TolC exit duct that projects an α-helical tunnel across the periplasm. The TolC periplasmic entrance ...

    In bacterial drug resistance and virulence pumps, an inner membrane (IM) transporter and periplasmic adaptor recruit an outer membrane (OM) trimeric TolC exit duct that projects an α-helical tunnel across the periplasm. The TolC periplasmic entrance is closed by densely packed α-helical coiled coils, inner H7/H8, and outer H3/H4, constrained by a hydrogen bond network. On recruitment, these coiled coils must undergo transition to the open state. We present 2.9 Å resolution crystal structures of two sequential TolC open states in which the network is incrementally disrupted and channel conductances defined in lipid bilayers. Superimposition of TolC(RS) (370 pS) and TolC(YFRS) (1,000 pS) on the TolC(WT) closed state (80 pS) showed that in the initial open-state TolC(RS), relaxation already causes approximately 14° twisting and expansion of helix H7 at the periplasmic tip, increasing interprotomer distances from 12.2 Å in TolC(WT) to 18.9 Å. However, in the crystal structure, the weakened Asp(374) pore constriction was maintained at the closed state 11.3 Å(2). In the advanced open-state TolC(YFRS), there was little further expansion at the tip, to interprotomer 21.3 Å, but substantial movement of inner and outer coiled coils dilated the pore constriction. In particular, upon abolition of the TolC(YFRS) intraprotomer Tyr(362)-Asp(153) link, a redirection of Tyr(362) and "bulge" in H3 allowed a simple movement outward of H8, establishing a 50.3 Å(2) opening. Root mean square deviations (rmsds) over the coiled coils of the three protomers of TolC(RS) and TolC(YFRS) illustrate that, whereas independent movement at the periplasmic tips may feature in the initial stages of opening, full dilation of the pore constriction is entirely symmetrical.


    Organizational Affiliation

    Department of Pathology, Cambridge University, Cambridge CB2 1QP, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OUTER MEMBRANE PROTEIN TOLC
A, B, C
428Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: tolC (colE1-i, mtcB, mukA, refI, toc, weeA)
Find proteins for P02930 (Escherichia coli (strain K12))
Go to UniProtKB:  P02930
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A, B, C
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.258 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 124.690α = 90.00
b = 135.220β = 90.00
c = 136.470γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance